Rahul Nayak
A Bioinformatician
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WhatsHap: fast and accurate read-based phasing
By Jit 2402 days agowhatshap.readthedocs.io - WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Features Very accurate...ANItools web: a web tool for fast genome comparison within multiple bacterial strains
By Jit 2232 days agohttp://ani.mypathogen.cn/ - ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1698 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 133 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...Heatmapper: web-enabled heat mapping for all
By Jit 2276 days agowww2.heatmapper.ca - Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Heatmapper is a versatile tool that allows users to easily create a wide variety...Scientists map 17,294 proteins produced in human body
By Jit 3862 days ago17,294 proteins mapped in 30 organs of human bodyMOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3140 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
By Jit 2033 days agohttps://fuma.ctglab.nl/ - FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results. The SNP2GENE function takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic...Introduction to programming. Write short programs that generate graphics and animation.
By Ram Yash Pal 3784 days agoShort programs that generate graphics and animation.GffCompare: Program for processing GTF/GFF files
By Jit 1995 days agoccb.jhu.edu - The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).
